

####################################################################################
## CDS区突变负荷的比较
${Rscript} ${scripts_path}/comparePublicData/CompareBurden.publicData.R \
--njmu_file ${work_dir}/baseTable/STAD_Info.addBurden.tsv \
--tcga_file ${work_dir}/public_ref/TCGA/TCGA_STAD.TMB.tsv \
--oncoSG_file ${work_dir}/public_ref/OncoSG/OncoSG_STAD.TMB.tsv \
--out_path ${Images_path}/comparePublic

####################################################################################
## 公共数据比较驱动基因在IGC和DGC的突变率
for Gene in `cat ${mutsig_check_path}/smg.list | grep -v Gene_Symbol | sort -u`
do
echo ${Gene}
## mutRate作图
${Rscript} ${scripts_path}/comparePublicData/OncoSG_mutRate_plot.TP53.R \
--Gene ${Gene}  \
--stad_mut_rate_dgc ${work_dir}/public_ref/OncoSG/OncoSG_STAD_DGC.mut_rate.tsv \
--stad_mut_rate_igc ${work_dir}/public_ref/OncoSG/OncoSG_STAD_IGC.mut_rate.tsv \
--images_path ${Images_path}/comparePublic
##mutRate作图
${Rscript} ${scripts_path}/comparePublicData/TCGA_mutRate_plot.TP53.R \
--Gene ${Gene}  \
--stad_mut_rate_dgc ${work_dir}/public_ref/TCGA/TCGA_STAD_DGC.mut_rate.tsv \
--stad_mut_rate_igc ${work_dir}/public_ref/TCGA/TCGA_STAD_IGC.mut_rate.tsv \
--images_path ${Images_path}/comparePublic
done

Gene=TP53
## 突变负荷的比较
## OncoSG
${Rscript} ${scripts_path}/comparePublicData/OncoSG_mutBurden_plot.TP53.R \
--input_file ${work_dir}/public_ref/OncoSG/OncoSG_info_include_mut.tsv \
--TMB_raw_file ${work_dir}/public_ref/OncoSG/OncoSG_STAD.TMB.tsv \
--images_path ${Images_path}/comparePublic
## TCGA
${Rscript} ${scripts_path}/comparePublicData/TCGA_mutBurden_plot.TP53.R \
--input_file ${work_dir}/public_ref/TCGA/TCGA_info_include_mut.tsv \
--TMB_raw_file ${work_dir}/public_ref/TCGA/TCGA_STAD.TMB.tsv \
--images_path ${Images_path}/comparePublic

####################################################################################
## 我们鉴定的驱动基因突变率的比较
## 所有的TCGA人群
## MutRate.compare_TCGA.DriverGene.pdf
${Rscript} ${scripts_path}/comparePublicData/TCGA_mutRateCompare_select_9_partscript.R \
--TCGA_rate_file_DGC ${work_dir}/public_ref/TCGA/TCGA_STAD_DGC.mut_rate.tsv \
--TCGA_rate_file_IGC ${work_dir}/public_ref/TCGA/TCGA_STAD_IGC.mut_rate.tsv \
--njmu_rate_file ${work_dir}/images/mutRate/MutRate.tsv \
--tumor_type STAD \
--show_file ${mutsig_check_path}/smg.list \
--out_path ${Images_path}/comparePublic

## TCGA白人
## MutRate.compare_TCGA_white.DriverGene.pdf
${Rscript} ${scripts_path}/comparePublicData/TCGA_mutRateCompare_select_9_partscript_white.R \
--TCGA_rate_file_DGC ${work_dir}/public_ref/TCGA/TCGA_STAD_DGC.mut_rate.tsv \
--TCGA_rate_file_IGC ${work_dir}/public_ref/TCGA/TCGA_STAD_IGC.mut_rate.tsv \
--njmu_rate_file ${work_dir}/images/mutRate/MutRate.tsv \
--tumor_type STAD \
--show_file ${mutsig_check_path}/smg.list \
--out_path ${Images_path}/comparePublic

## Oncosg
## MutRate.compare_OncoSG.DriverGene.pdf
${Rscript} ${scripts_path}/comparePublicData/OncoSG_mutRateCompare_select_9_partscript.R \
--OncoSG_rate_file_DGC ${work_dir}/public_ref/OncoSG/OncoSG_STAD_DGC.mut_rate.tsv \
--OncoSG_rate_file_IGC ${work_dir}/public_ref/OncoSG/OncoSG_STAD_IGC.mut_rate.tsv \
--njmu_rate_file ${work_dir}/images/mutRate/MutRate.tsv \
--tumor_type STAD \
--show_file ${mutsig_check_path}/smg.list \
--out_path ${Images_path}/comparePublic


####################################################################################
## 已报道的驱动基因突变率的比较
## MutRate.compare_TCGA.ReportGene.pdf
${Rscript} ${scripts_path}/comparePublicData/TCGA_mutRateCompare_all.R \
--TCGA_rate_file_DGC ${work_dir}/public_ref/TCGA/TCGA_STAD_DGC.mut_rate.tsv \
--TCGA_rate_file_IGC ${work_dir}/public_ref/TCGA/TCGA_STAD_IGC.mut_rate.tsv \
--njmu_rate_file ${work_dir}/images/mutRate/MutRate.tsv \
--tumor_type STAD \
--show_file ${work_dir}/public_ref/SMG_sort.list \
--out_path ${Images_path}/comparePublic

## MutRate.compare_OncoSG.ReportGene.pdf
${Rscript} ${scripts_path}/comparePublicData/OncoSG_mutRateCompare_all.R \
--OncoSG_rate_file_DGC ${work_dir}/public_ref/OncoSG/OncoSG_STAD_DGC.mut_rate.tsv \
--OncoSG_rate_file_IGC ${work_dir}/public_ref/OncoSG/OncoSG_STAD_IGC.mut_rate.tsv \
--njmu_rate_file ${work_dir}/images/mutRate/MutRate.tsv \
--tumor_type STAD \
--show_file ${work_dir}/public_ref/SMG_sort.list \
--out_path ${Images_path}/comparePublic



####################################################################################
## CNV突变率的比较